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"cells": [
{
"cell_type": "markdown",
"id": "a1be4f68",
"metadata": {},
"source": [
"# Figure 4A: predicted vs measured solvent-induced shift, implicit (PCM)\n",
"\n",
"Implicit (PCM) predicted vs measured solvent-induced shifts (Δδ vs. CDCl3, ¹H) for one solvent per class."
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "27283d57",
"metadata": {},
"outputs": [],
"source": [
"import os, sys\n",
"\n",
"# make the in-repo modules importable (not pip-installed)\n",
"REPO = os.path.abspath(\"../..\")\n",
"for _p in (\"data/delta22\", \"analysis/code\", \"analysis/code/shared\"):\n",
" sys.path.insert(0, os.path.join(REPO, _p))"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "576ad573",
"metadata": {},
"outputs": [],
"source": [
"import delta22\n",
"import paths\n",
"import fig4_plots"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "fff8d490",
"metadata": {},
"outputs": [],
"source": [
"DELTA22_HDF5 = paths.dataset_file(\"delta22\", root=REPO)\n",
"XLSX = os.path.join(REPO, \"data\", \"delta22\", \"delta22_experimental.xlsx\")\n",
"\n",
"def figure_path(name):\n",
" os.makedirs(\"figures\", exist_ok=True)\n",
" return os.path.join(\"figures\", name)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "236a76a8",
"metadata": {},
"outputs": [],
"source": [
"METHOD, BASIS, GEOM = \"b3lyp_d3bj\", \"pcSseg2\", \"aimnet2\"\n",
"q = delta22.load_query_df_dft(DELTA22_HDF5, XLSX, verbose=False)\n",
"one = q[(q[\"sap_nmr_method\"] == METHOD) & (q[\"sap_basis\"] == BASIS) & (q[\"sap_geometry_type\"] == GEOM)]\n",
"one = delta22.add_solvent_mean(one)\n",
"print(len(one), \"rows for\", METHOD, BASIS, GEOM)"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "f28bd2a4",
"metadata": {},
"outputs": [],
"source": [
"shifts_chcl3 = delta22.solvent_induced_shifts(one, \"chloroform\", delta22.DESMOND_SOLVENTS,\n",
" nucleus=\"H\", explicit=\"desmond\")\n",
"print(len(shifts_chcl3), \"site/solvent differences\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "6f3c02f9",
"metadata": {},
"outputs": [],
"source": [
"# Water == TIP4P\n",
"FIG4_HIGHLIGHT = {\"dimethylsulfoxide\": \"DMSO\", \"TIP4P\": \"Water\", \"benzene\": \"Benzene\"}\n",
"FIG4_ORDER = [\"DMSO\", \"Water\", \"Benzene\"]\n",
"FIG4_PALETTE = {\"DMSO\": \"#61a89a\", \"Water\": \"#A72608\", \"Benzene\": \"#dacd82\"}\n",
"FIG4_MARKERS = {\"DMSO\": \"o\", \"Water\": \"^\", \"Benzene\": \"X\"}"
]
},
{
"cell_type": "code",
"execution_count": null,
"id": "59bb0a61",
"metadata": {},
"outputs": [],
"source": [
"fig4_plots.save_panel(\n",
" lambda ax: fig4_plots.draw_shift_scatter(ax, shifts_chcl3, \"implicit_diff\",\n",
" FIG4_HIGHLIGHT, FIG4_ORDER, FIG4_PALETTE, FIG4_MARKERS),\n",
" figure_path(\"fig4a_implicit_1H.png\"),\n",
")"
]
}
],
"metadata": {},
"nbformat": 4,
"nbformat_minor": 5
} |